Lines of Code
[root]/src/dr/evomodel/arg/operators
| Author | Changes | Lines of Code | Lines per Change |
|---|---|---|---|
| Totals | 74 (100.0%) | 9494 (100.0%) | 128.2 |
| msuchard | 16 (21.6%) | 5667 (59.7%) | 354.1 |
| alexei.drummond | 9 (12.2%) | 2472 (26.0%) | 274.6 |
| bloomquist | 17 (23.0%) | 1038 (10.9%) | 61.0 |
| rambaut | 15 (20.3%) | 255 (2.7%) | 17.0 |
| jheled | 12 (16.2%) | 58 (0.6%) | 4.8 |
| dong.w.xie | 5 (6.8%) | 4 (0.0%) | 0.8 |
ARGAddRemoveEventOperator updated to handle two partitions
373 lines of code changed in 2 files:
Some refactoring of MatrixParameter (renamed getNumberOfParameters to getParameterCount). Also allowed MultivariateNormalPrior take a matrix parameter and assume the individual parameters within this represent independent draws from the MVN.
3 lines of code changed in 6 files:
Decoupled the process of checking node heights are within bounds to confirm that an operator is correct from using it to reject a move. By default tree moves just call treeModel.endTreeEdit() to finish editing the tree. If they need to check whether the resulting tree is valid they can call checkTreeIsValid() which throws an exception if not. Most moves do not need this check if correctly implemented. Some I wasn't too sure about so I left the check in for those to give the same behaviour (but it is up to the operator whether this check is made and what to do about it).
TreeModel.endTreeEdit() can optionally make this test (switch on a flag at the top of TreeModel) but throws a runtimeException so stops the program if it fails.
252 lines of code changed in 9 files:
Trunk refactoring: organize tree and treelikelihood parsers.
4 lines of code changed in 5 files:
automatic intelliJ stuff
6 lines of code changed in 1 file:
get rid of cyclic dependency. Add setting of population sizes to initial species tree.
3 lines of code changed in 2 files:
automatic idea changes, change type return type of getChild
39 lines of code changed in 4 files:
A small improvment in reducing usage of litteral string constants.
Each constant should be defined in one place and referenced elsewhere.
The best place I found is in the various parsers. This may be wrong but now moving it elsewhere is a simple matter.
9 lines of code changed in 4 files:
Made the AddRemoveOperator backwards compatible for the rate variation stuff.
33 lines of code changed in 1 file:
ARGModel now fully supports caching partial likelihood calculations even as nodes are added and remove from tree. Support is not fully implemented in the operators yet.
7 lines of code changed in 2 files:
Started overhaul of ARG model likelihood calculations to cache unaffected partials (it's about time I did this). All changes to the ARG model, except for topological changes, appear to be caching correctly; speed-up is about 30% (for a small example, suspect much more for larger problems). I need to think harder about how to handle topological changes -- a simple map from old ARGTree nodes to ARGModel to new ARGTree nodes should suffice.
44 lines of code changed in 2 files:
automatic idea changes
1 lines of code changed in 1 file:
Rate variation appears to be working. In fact, it seems to be working very well! For now, old arg stuff will not work, but will fix as soon as possible.
30 lines of code changed in 1 file:
Forgot to add these new classes.
14 lines of code changed in 1 file:
Not positive yet, but fairly sure have joint rate variation estimation and ARG inference working.
21 lines of code changed in 1 file:
Ok, I think I got it! This one actually sampled correctly.
25 lines of code changed in 1 file:
Let in some debug stuff on accident.
5 lines of code changed in 1 file:
Made major fix to ARGAddRemoveOperator.
585 lines of code changed in 1 file:
Modified some minor ARG Stuff. Added statistic to give total ARG length.
5 lines of code changed in 2 files:
Added the ability to flip multiple partitions at once in arg model.
31 lines of code changed in 1 file:
Modifications to the ARG package.
2 lines of code changed in 2 files:
Added a partition likelihood for ARGModel
143 lines of code changed in 2 files:
Fixed some bugs.
138 lines of code changed in 2 files:
Added removeParameter functionality to CompoundParameter to faciliate removal of ARGCompoundParameter and VariableSizeCompoundParameter classes to integrate the ARG code more fully. A small success for simplification against the growing tide of class proliferation!
282 lines of code changed in 5 files:
added variable size functionality to Parameter
2190 lines of code changed in 4 files:
Changed the parser so it adds the weight.
6 lines of code changed in 1 file:
Port of ARG classes into the trunk. There are some very silly repeats of code (namely: TreeModel and ARGModel should inherit from a base class, ARGTreeLogger is almost indentical to TreeLogger, and CompoundParameter should replace ARGCompoundParameter).
5243 lines of code changed in 10 files: